TMNT - The Alien Agenda
by Ithilear
Summary: Raph and Leo both think they know what's going on in Karai's head. Is either of them right? Or does she have motivations they know nothing about? (Rated T just to be safe)
1. Show Off

**TMNT – The Alien Agenda – Chapter 1 – Show Off**

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 **The next episode! Hope you enjoy!**

 **Feedback welcomed and appreciated!**

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Karai walked slowly along the roof, waiting for the half-dozen Foot soldiers in her squad to catch up to her.

 _I'm not sure which I'm hoping for more,_ Karai thought to herself. _That we find Leo and his brothers, or that we don't. If I was alone, that would be one thing, but..._

As the last straggler came up, she turned to face the group of ninja and placed her fists on her hips. "The turtles have been spotted in this neighborhood," she ordered, "So stay alert for any sign of them." Before she finished speaking, sounds of strange gunfire came from the alley behind her, punctuated by voices, and the occasional, "Booyakasha!"

 _...It's them_.

The other Foot looked toward the edge of the roof to see what the commotion was, but she held up a hand to keep them from approaching. She wanted to assess the situation before they rushed in. It was no use jumping into a fight you couldn't win.

Karai stepped over to the edge and looked down. What she saw astonished her – and she wasn't easily surprised. The four green ninja were rolling, flipping, and expertly dodging purple laser blasts being fired by a dozen or so...what were those things? "When fight is concluded the ones called the turtles are defeated by Krang," said a computerized voice. She watched as Leonardo cut the arms off one of their opponents. It fell to the ground with a metallic _CLANK_. "They're fighting robots?"

The Foot ninja stepped toward her to see for themselves, but she held up a hand again to stop them. As Karai watched the armless robot lying on the pavement, a magenta-colored, brain-shaped creature sprouted tentacles, pulled itself out of the robot's abdomen, and crawled away, squealing like a pig. "Whoa!" she exclaimed. "This town's more interesting than I thought!"

There was no way Leo heard Karai speaking over all the noise of the battle; maybe he just sensed that they were being watched. For whatever reason, at that moment, he looked up and saw her standing on the edge of the roof. The distance was nothing to him. He knew her eyes were on him, and he instantly smiled. _I was wondering when we'd meet again_.

Leo turned back to the fight with a grin. _Now's my chance to REALLY show her what I'm made of_. He pulled out all stops and used his best moves. Flipping onto the head of one Krang-bot and crushing it, he sliced through its blaster with his katana before it hit the ground. "I'll save you, Raph!" he said heroically, jumping between his more than capable brother and the bot he was fighting, and slicing the latter's chest in two. " _YOU'LL_ save?!" Raph called after Leo angrily.

Leo wasn't listening. He was already bounding off the wall to take out another bot with a front kick-round kick combo. Leaping onto the bot Mikey had already chained up with his kusarigama, Leo shouted over the din, "Relax, Mikey!" He sliced the arms off the bot; it crumpled beneath him. "You're safe now." He glanced up at Karai with a smirk. She arched a brow. "Thanks!" Mikey said happily, before thinking about what had just happened and frowning. "Wait...I was fine!" Raph glared at Leo and grumbled. _There's gotta be some reason he's showing off like this_.

"Donnie! Behind you!" Leo cried.

"Huh?" Donatello quickly turned to see what Leo was warning him of. "...The wall...?"

By the time Donnie looked back to the two Krang-bots he had been fighting, Leo had taken out both. He flipped sideways away from Donnie, did a quadruple back-flip through the air, landed near Raph and Mikey, and sheathed his katana smoothly. Leo glanced up at Karai with a cocky smirk, thinking, _How d'you like me now?_ He felt gratified when her eyes went wide. Raph followed Leo's gaze up to the rooftop, and saw her just before she scrambled out of view.

"Uh, what the heck was that?" Donnie asked, walking up to their team leader. Mikey pushed his way past Donnie and Raph and asked accusingly, "Yeah, are you trying to impress us?" He ran to hug his big brother. "'Cause it totally worked!" He squeezed Leo's cheek.

Donnie caught Raph glowering at Leo and asked, "What is it, Raph?"

"I thought I saw something." He stepped closer to Leo. "What about you, Leo? Did _you_ see something?"

"No." Leo lifted his hands innocently, but his tone said otherwise.

Raph folded his arms and narrowed his eyes. "Turtles first, right?"

Leo answered almost grudgingly. "Turtles first." He and Raph stared at each other angrily, eyes smoldering.

"Do you feel like we're missing something?" Donnie asked Mikey.

"All – the – time."

…

Back at the lair, Raph and Leo were combining a heated discussion with some serious sparring.

"You _knew_ the Foot Clan was watching us!"

"Not the Foot – Karai!"

"Karai _IS_ the Foot!" The brothers growled at each other and locked weapons.

"You _knew_ she was watching and all you did was show off!"

Leo rolled onto his back and kicked his brother up and over him. He got up and faced Raph. "I was demonstrating how formidable we are. I knew she wasn't going to attack us." He smirked. Raph circled him slowly. "Of course not! She's studying our moves for next time. You don't flirt with the enemy, Leo. You take 'em down."

"No! You're wrong about her! She _has_ a good side!" Leo insisted. They locked weapons again.

"Oh yeah? If _that's_ what you're doing why don't you go tell the others?"

"Because they wouldn't understand."

Raph pushed Leo into the wall and held him there with his arm across the top of his plastron. "You really think Mikey and Donnie wouldn't understand?" Raph glanced away for a moment, reconsidering. "You really think Donnie wouldn't understand?"

"Look! I know what I'm doing!" Leo didn't want to hear any more of this. He sent Raph flying across the room with a palm-heel strike. Raph wasn't going to take that lying down. He tackled Leo and took him to the ground hard, punching his chest twice before being thrown off. "Yah!" Leo flew through the air and tackled Raph from behind, putting him in a head lock. "You _have_ to trust me."

"Why should I?!"

"What is going _on_ in here?!" Their master's stern voice came from the doorway to the dojo. Both sets of eyes went wide seeing Splinter now standing before them and eying them suspiciously. The ninja quickly rose to their feet.

"Ahh, nothing important..." Leo glanced at his brother. "Right, Raph?"

Raph folded his arms and looked away angrily, but finally sighed in defeat. He wasn't going to rat his brother out like this. Not yet. _I'll give Leo a little more time to wise up before I go telling the others_. His voice was resigned: "Right." He shouldered Leo and glared at him as he walked away.

Leo's shoulders slumped. _What am I doing? ...Maybe Raph IS right. Maybe she is just toying with me before going in for the kill; playing cat-and-mouse. How can I be sure?_ He walked quietly out of the dojo. _I truly believe there is goodness in her, but...it's not worth risking my family if I'm wrong. I need to know that whatever happens between us, she won't hurt them._ He made up his mind. _Tomorrow night, I'll go alone. I'll find her. And make sure she knows what will happen if she ever comes after my family._

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(Author's note: Sorry for the re-write! I know this episode very well, but when I wrote this, I forgot that Leo and Karai meet up the _next_ night, not the same night as the bot-fight. Had to fix that! Next chapter should be up tonight or tomorrow! Thanks for reading!)


	2. Karai's Mission

**TMNT – The Alien Agenda – Chapter 2 – Karai's Mission**

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 **Thanks for reading! Feedback welcomed and appreciated! :)**

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"Heh, heh, heh. Aww, the mermaid's growing legs!" Dogpound chuckled.

Baxter Stockman glared at him. "Please! Settle down." He looked to the fish mutant whose robotic legs he had been adjusting. "Xever, get ready to walk," he said dramatically.

Xever began stepping haltingly about Shredder's "throne room"; he managed only five steps before the legs glitched. Without warning, they broke into a run, sending him flopping onto his back and dragging him along the floor until running him smack into the wall. They reversed direction, now running straight up the stairs to Shredder's throne and into the window behind it. Dogpound laughed his head off; Baxter winced. This would mean not only a very unhappy Xever, but an infuriated Shredder.

Xever lay on his stomach against the window as his legs kicked and flailed of their own will, occasionally smacking him in the face. "Fix this!" Xever exclaimed between kicks, "Or I will bite your head off!" Baxter pushed a button on the remote console in his hands, and the legs powered down. Just then, the doors to the room swung open, admitting none other than the Shredder.

" _Baxter Stockman_." He did not sound pleased.

Baxter's head whipped around to see his fearsome boss standing behind him. "Mr. Shredder!" he yelped, then asked nervously, "H-how long have you been standing there...?"

"Long enough to witness your failure," came the stern reply. He narrowed his eyes at the scientist. "My patience is wearing thin."

"Yes, sir," Baxter answered quickly. "It's just, the control mechanism is proving trickier..."

"Enough!" Shredder cut his reply short. He didn't notice his crouched daughter watching and listening from the window ledge above the double doors behind him. "If he isn't walking soon... _you won't be either_. I will give you one more chance, and _then_ I..."

"Father." Having jumped silently from her position to the floor, she rose and interrupted before Shredder had a chance to finish threatening the enslaved genius. He turned to face his daughter as she approached. "We spotted the turtles fighting some guys in suits. But they were actually slimy brain-squids in robot bodies!"

"Your mission is to destroy them and find Splinter! Everything else is a distraction!" he replied severely.

"Distraction?" She said incredulously. "Father, don't you want to know what's going on? Robots and creatures? Splinter's disciples are turtles; mutants! Your own men got turned into hideous freaks! Don't you think we should be finding out what's going on? I mean, there's more to life than your vendetta."

"There is _NOTHING_ more!" Shredder walked around Karai to stand behind her, placing a hand on her shoulder. "Have you forgotten what he did to me? To _us_?" She looked away, sadly. _Splinter is the reason I grew up without my mother_. He stepped in front of her to face her again. "Every day that Splinter lives is a stain on our honor that we must wipe clean! Stay focused on your mission, Karai."

Her expression became grave. "Yes, Father." She turned away, replaced her face mask, and walked determinedly from the room to complete her mission.

A mission Shredder knew nothing about.

…

 _I have to help him_.

The following night, Karai paced silently in the deep shadows of a remote rooftop, far removed from the Foot Clan HQ.

 _My father doesn't make idle threats. If he says time is running out for Baxter – he means it. And what he's asking of him is no small task. Creating robot legs for a fish mutant that are neurologically connected to his own brain? He's made a good bit of progress so far, but if he doesn't fully provide what Xever needs to walk again, he WILL end up crippled. Or worse._

She half-smiled to herself. _Last night, I just happened to see some highly advanced robots, being controlled perfectly by those brain-squid things. I bet that if Baxter had access to one of those bot-bodies, he'd have the parts he needs, and he's smart enough to figure out how to apply the technology to Xever's mechanical legs. He and Xever would both be useful to my father again...and they'd both get to live._

Karai caught a movement out of the corner of her eye. She turned to see what it was, but remained hidden in the shadows. It was silent, swift, avoiding the light. But, for a moment, she saw a flash of green.

 _It's him_.

She left her own hiding place to tail the turtle at a distance. It took one very skilled ninja to follow another without observation. She could make out two narrow, red objects on his back. _Definitely Leo_. She smiled to herself. _I wonder if he's looking for me...?_

At last Leo stopped on the well-lit rooftop of a building in Chinatown. He stood in the open now, his hands on the roof's edge, peering down to the street below. She watched, and waited. _We'd better not be spotted by any Foot soldiers. That could be disastrous for me...and others._ Having scanned the surrounding area for twenty minutes and feeling that they would be safely unobserved, Karai hastened toward him.

Leo yawned. He needed to get back to the lair before much longer. _Before Raph starts to suspect where I've gone...and why._ A _thump_ came from the building's water tower behind him. His eyes went wide. _She's here._

Leo pulled his katana from their sheaths and turned to face the kunoichi. There she was, crouched high in the moonlight, just like the first time he saw her. "How'd I know you'd show up?" His tone wasn't friendly, and was edged with suspicion. She couldn't really blame him. They were still enemies, after all.

Karai rose to her feet. "'Cause you're not good at hiding from me?" Even with her mask on, he could hear her smiling. _She's playing with me again_ , Leo thought. "Like last night," he retorted, unable to resist a slight smirk.

"Oh, were you there? I didn't notice," she answered coyly. "I did see a bunch of robots, though. What's their deal?"

"Their deal is they're incredibly dangerous. Stay away from them." He pointed a katana at her as a warning.

She answered playfully: "I like them already." Her tone suddenly became serious. "Something else is going on. What is it?"

"I'm not sure I should tell you any more. Raphael says I can't trust you."

Karai arched a brow. "He makes a good point." She flipped through the air and landed on the roof with her right leg bent and left leg extended, left hand touching the blacktop. Her agility really was quite remarkable, but Leo wasn't in the mood to appreciate it. He sheathed one sword in an instant and held the other with both hands, ready. From her landing position, she narrowed her eyes at him. "Eventually I am going to destroy you."

She grasped the tanto at the back of her waist and unsheathed it while lunging toward Leo. He ran to meet her, and their blades clashed. "I don't think you are!" he protested. She laughed and twirled her sword from one hand to the other. "Really? And what do you think _THIS_ is?" She attacked.

"I think it's a cry for help," Leo answered astutely. They exchanged more blows. "I think you're looking for a way out of the Foot Clan. And _I_ can help you." Had she not been so thoroughly trained to keep her emotions hidden, she might have blinked in shock at his shrewd reply. _Can he really see through me so well_? she thought. The night they met, she had tested him to see if he could ever leave the pure whiteness of his current life so she could leave the blackness of hers, and they could fight, and live, in the gray area between them. _Without a friend like him to have my back...there's nowhere for me to go._ Pushing these thoughts aside, she laughed and then growled playfully at him, "You're _adorable_. Stupid, but adorable."

Leo was stunned and momentarily disarmed. He blinked with an innocent smile he couldn't keep from creeping to his lips. "R-really? Y-you...you think I'm...? Yah!" He yelped as she rushed in to strike while he was still stammering. A second later she was leaping from water tower to water tower, roof to roof. He watched her for a moment before giving chase, cutting her off atop a large building. He wasn't sure what she was playing at, but now he'd had enough.

"You wanna play games?" He glared at her. " _I_ can handle it." His voice became soft, and serious: "But I need your word that you will not attack my brothers."

"You know I can't do that." They both yelled and lunged at each other. Their swords crossed, and Leo snarled at her between them, "Then understand this. You come after them, _I'll_ come after you. _Hear me?!_ "

Karai slid her blade away from his and tumbled acrobatically away from him toward the far edge of the roof. She pulled her mask away from her face, looked at him, and smiled. "Loud and clear." Replacing the mask, she jumped backwards off the roof. Leo ran to the edge to look down after her, but she was already gone. He sheathed his sword thoughtfully. _At least now we have an understanding._

…

Karai was lost in thought as she stealthily made her way back to Shredder's lair. _He sees me much more clearly than I thought_. She was still surprised at the depth of Leo's insight into her motives for that midnight rendezvous, when she had tempted him with the sword of Miyamoto Musashi. He must have surmised then that she wanted him on her team. Not Shredder's. _Mine_.

She had hoped he would answer her questions about those robots. _No such luck. He doesn't trust me enough to share information, even about his enemies. And yet, he did warn me to stay away from them. Is he concerned FOR me, or just hiding something FROM me?_

It seemed Karai would have to find a different way to learn more about those robots, and get what she – well, Baxter and Xever – needed from them. She already knew who could lead her to them. And, like she had said – he wasn't good at hiding from her.


	3. The Worldwide Genome Project

**TMNT – The Alien Agenda – Chapter 3 – The Worldwide Genome Project**

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 **Thanks for reading! Feedback welcomed and appreciated!**

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"So what the heck _is_ that thing?" April asked as she, Leo, and Donnie all looked down at the sizzling, electrocuted form of the robotic old lady who had attacked her in the middle of school.

"Looks like a Krang droid...minus the Krang," Leo answered slowly. They had never seen a robot like this one before.

"She said she was from the Worldwide Genome Project."

"Whoa." Mikey held the robot's feminine face plate over his face like a Halloween mask. "How did the Krang know that you sent your DNA spit to the Worldwide Thingamajig Project!?" Raph glanced over at him and cried out in surprise. For a second, he thought that tough old-lady bot with missile-launching elbows was back for another fight. He growled at Mikey for scaring him, then whacked the mask out of Mikey's hands (while simultaneously smacking him in the face).

"They must have hacked into their system," Donnie surmised. "Who knows what kind of information they could be stealing?

"April, you'd better head to the lair where it's safe. We'll go check out the Worldwide Genome Project."

April nodded her agreement to Leo.

"But first, we gotta take down the East-side High Panthers," Mikey added, looking at a poster of a "Roosevelt High Viking" stomping a black panther. He turned to face April and his brothers. "According to that poster, they've got it coming."

Everyone (but Mikey) blinked.

…

That night, the four green ninja leaped silently from building to building with Leo taking point. Of course they were alert, but also thoroughly enjoying themselves. Getting out of the sewers at night and being able to move swiftly and freely above ground was liberating. Mikey in particular took pleasure in being goofy as he jumped and ran, making random silly faces along the way. Raph and Donnie were enjoying the exercise, which could be seen as a warm-up for what would probably be a fight at some point during the night. But Leo was immersed in their mission. He had no room for distraction or silliness of any kind. It was his prerogative, and his duty, to be supremely focused. To a fault.

Leo never noticed the black and armor-clad kunoichi tailing them, staying far back enough to keep from being seen or heard. Karai wasn't exactly sure of their destination; only their general direction. She couldn't know whether their operation had anything to do with the Krang, yet. All she could do was wait and see.

The turtles stopped at last on a rooftop with an electronically locked door leading to the building below. She couldn't hear what was said, but guessed that they were about to pick the lock. _Breaking and entering, huh?_ She grinned wickedly behind her mask. _Not such a goody-three-toes after all, are we?_

Raph and Donnie approached the door first. The former asked the latter, "So how do we get in?"

"Leave it to me." Donnie whipped an electronic key card out of his belt. "I've got an app for that."

His brothers groaned. "Oh, boy," Leo said in exasperation. Donnie was certainly a genius, but still, incredibly nerdy. He inserted the device into the key card slot and began punching buttons on a tiny console. Raph leaned down to his brother and said in his face, "I've got an app for that, too." He backed up a step, then flying front-kicked the door wide open with a loud _BANG_. Donnie frowned. Raph was always too impatient to ever let him use the cool contraptions he'd invent just for such missions as this one. The turtles filed inside one by one, with Donnie bringing up the rear. As the door swung shut behind him, a dark figure landed on the AC units near the roof's edge. Karai narrowed her amber eyes. _What could they be doing in a place like this – The Worldwide Genome Project_?

Leo, Raph, Donnie, and Mikey crept along the darkened halls inside the building. The wall to their left had illuminated pink signs reading "W.G.P." every few feet; on their right were various sensors and consoles with magenta lights that looked very familiar. Mikey eyed their surroundings warily. "You know, for a human lab, this place is awfully Krang-y..." he observed aloud. "Guys," Leo whispered urgently, "I think the Krang _are_ the Worldwide Genome Project!"

The ninja entered a huge, round room with a giant vat of glowing, sea-green mutagen surrounded by keypads and consoles in the center. Two Krang bots with transparent, blue, artificial flesh covering their metallic frames approached one another, each holding a laser blaster. They heard a sound coming from the elevator and approached it...then looked back over their shoulders. Strange noises were suddenly coming from different parts of the lab. The bots didn't speak a word, but communicated with each other using computerized noises that sounded as if they were chattering together in an alien language.

Mikey appeared before them out of nowhere and whispered in one bot's face: "...Booyakashaah."

Donnie jumped into the air spinning his bo staff; he came down on the bots' heads with a yell. Both droids quickly immobilized, they were thrown into a side room and locked in. The brain-like Krang creatures popped out of their robotic housing and stuck to the glass of the door, squealing furiously at their captors. Raph pointed at them through the glass and smirked, "Now you two place nice in there."

"What are those?" Leo asked Donnie. They were both looking at the outer wall of the circular lab, which was covered in differently-colored columns, each marked with the picture of an animal. "Well, it looks like they're collecting DNA from every plant and animal species on Earth!" Donnie replied.

"What?!"

"Building blocks, dude. Pshh," Mikey chimed in patronizingly. "I'll drop the science on you later."

"I wonder what they're doing with all this DNA?" Donnie wondered.

Leo balled up his fists determinedly. "Whatever it is, it can't be good. Let's shut this place down!"

"Hey, where's Raph?"

Mikey's query was promptly answered by a _whack_ and Raph's voice coming from above them. "Gotcha!"

The three looked up to see Raph land on the sealed top edge of the mutagen vat with a lightly armored kunoichi beneath him, locked in his grip. She raised her head enough to look at Leo. "Karai!"

"Ka-who?" Donnie was puzzled.

"Bet you think you're pretty slick?" Raph grinned in her ear. She made no answer, but twisted the wrist Raph was holding so that she now gripped his hand instead. Karai yanked him sideways and stood up, throwing him off her back in a blur. Before he landed, she raised one leg in a vertical split, and slammed her foot down on his plastron, forcing him to land hard on his shell with a loud _THUMP_ _._ She looked down at him with her head held high and said silkily, "I have my moments."

Raph growled, and the two flipped away from each other...but only for a moment. A second later, they were lunging at one another again. Karai expertly dodged his sai with her tanto still sheathed. Then drawing her blade, she side-kicked him away from her, counterattacked with her short sword, and their weapons locked. The pair glared at each other.

"Raph! Karai! Stop it!" Leo yelled up at them.

"Okay, _what_ the heck is going on here...? How do they _know_ her?!" Donnie turned to Mikey, wondering if his little brother knew more about this than he did.

"Yeah, and how do _we_ know her!" Mikey exclaimed. "Wait...do we know her?" he asked Donnie. Donnie sighed.

"So _this_ is the stuff that turns people into monsters, huh?" Karai remarked casually as she and Raph continued to fight atop the vat of mutagen. "How's it work?" Their weapons locked again.

"Why don'tcha lean in a little closer, and I'll show ya," Raph retorted.

 _As you wish_. Karai forced their crossed weapons down and head-butted Raph hard enough to send him flying to the floor below. He stood and looked up at her, weapons ready. _No WAY I'm letting this chick get the best of me!_ She looked at him for a moment, then leaped into the air and flipped on her way down, preparing to land a kick to his face.

There was a clash of steel as she landed. " _ENOUGH!_ " Leo shouted over the clamor. He stood between the two brawling ninja, his twin katana blocking both Raph's sai and Karai's tanto. "You're gonna set off...!" He stumbled back from between them and rested a hand on a console to steady himself...which immediately sounded the alarm he was warning them of. "...one of those." He closed his eyes, indignant at his own blunder.

"Nice going, Leo!" Raph yelled at his brother over the blaring alarm. "You're protecting her? What is _wrong_ with you?! She is bad news."

"No, she's not!"

Karai leaned forward and gave Raph a menacing glare. "Yeah, I am."

The trio's gaze was drawn by the sudden hiss of automated doors opening smoothly. Dozens of Krang-droids began pouring into the lab, from the level above, and below. The turtles, and Karai, all tensed and stood prepared for battle, tightening their grip on their weapons as row after row of the aliens marched into place, stopped, and turned to face the intruders with blasters aimed at them. The monotonous robot voice of one Krang spoke up among the others.

"The ones who are not authorized by the authority of Krang to exist in this place will now be destroyed by Krang in this place."

Karai stood, tanto drawn, with the ninja quartet around her. Leo, Donnie, Mikey, and Raph all faced the Krang who spoke, and held their weapons before them. Mikey began spinning his nunchaku. Karai's eyes sparkled mischievously.

"This day just keeps getting better."

...

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(Author's note: Thanks for reading! I considered labeling this chapter, "Part 1", but decided to let chapters 3 and 4 be their own entities instead. This is a really big scene in the show, though, so to include the whole thing in one chapter would've been prohibitively long. Hope you're enjoying it so far! Chapter 4 should be up today or tomorrow, I hope! Thanks again for reading!)


	4. Heroes

**TMNT – The Alien Agenda – Chapter 4 – Heroes**

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 _Unsung hero: (noun) a person who makes a substantive yet unrecognized contribution;_

 _a person whose bravery is unknown or unacknowledged._

 _..._

The Krang laboratory was immediately filled with hundreds of hot pink laser blasts; the noise reverberated off the walls and echoed around the circular room. It was enough to give less trained and less seasoned warriors shell shock. Of course, it didn't faze Karai, or the turtles. They were teenagers, but they certainly weren't "newbies" in battle.

Karai launched a knife into the metal skull of the nearest Krang droid before jumping onto its chest with both feet. Leo was engaging another bot, but smiled giddily to have Karai fighting alongside him. "Look! See?" he called happily to Raph. "She's on our side!"

"Are you even listening to yourself...?" Raph replied over the din.

Karai was running toward a trio of bots, keeping her head low and avoiding the laser fire. "I like your brother, Leo." She leaped over the heads of the bots, landed neatly behind them in her signature stance (right knee bent, left leg extended), and sliced through the abdomens of all three with one swing of her blade. The robots dropped like flies around her. "He's almost as entertaining as you."

Raph spun to face her with a frown, and a twitching robot hand skewered on one of his sai. "Oh, when this is over, I'll show you how entertaining I can be."

The noise in the room died down without warning. The five ninja all looked 'round, wondering what the cause for this sudden lull in laser fire could be. The turtles moved together, their backs to the wall, and watched dismayed as a huge laser cannon was wheeled into the lab, escorted by at least another dozen Krang. "Krang is now arriving to provide the help that has been requested by Krang."

"We're trapped!" Leo exclaimed.

"No... _you're_ trapped," came that impish voice. The brothers looked past the Krang standing in front of them and saw Karai leaning causally against a console beneath the vat of mutagen. The Krang turned to face her, and they all saw the pointer finger of her left hand hovering over a square button. "What happens if I do... _this,_ " she said with relish. The turtles' eyes grew to the size of saucers.

"NO!" shouted Raph.

" _Don't do that_!" yelled Leo.

"Highly undesirable outcome," a Krang chimed in.

"Well now I gotta." Karai grinned devilishly behind her mask, and lowered her finger.

The square beneath her digit went from white and teal to red.

All around the circular room, black liquid began to shoot up the multicolored columns built into the wall. The DNA of all sorts of animals contained within the columns surged up, then across the ceiling and into the gigantic vat of mutagen; jellyfish, beetle, octopus, and viper, among others. Mikey held his head and screamed like a little girl as the "cat column" emptied its contents into the mixture.

Every creature in the room turned toward the vat and watched in horror as the rainbow of liquids combined with the glowing mutagen. Flashes of colored light lit up the room; steam and smoke began pouring off the now open top of the giant container. A large organism dragged itself up and over the vat's edge, landing on the floor with a wet _splat_. It was too obscured by billows of green smoke for anyone to determine what it looked like yet, but as it moved about the room, they could sense its enormity from the air it displaced.

Thick, muscled tentacles lashed out from the smoke and snatched one droid; then two; then one more. A huge tentacle shot out at Karai; she leaped out of its way and over to where the turtles stood as the smoke began to clear. The mutant looked like an octopus at its base with its eight appendages spread concentrically upon the floor. Above this was a bulbous, round, black...head?..with one eyeball the size of a beach-ball sticking out from either side. Behind these eyes were relatively small...bat wings? As Karai and the turtles stared at it, it gave a tiny kitten _Mew_.

"Awwww, he's so cute!" Mikey exclaimed.

He spoke a moment too soon. The dark, reddish-colored octopus base of its body stretched upward so that the creature was now at least 12 feet tall. The eyeballs that had previously been tucked close to its body were now outstretched on eight-foot optic nerves as thick as a man's arm. The main cavity of its...torso...split open into a gaping, triangular mouth; as it roared, its tongue lashed out between two viper fangs, each a foot long, protruding from the base of its orifice.

The Krang opened fire on the mutant. It seemed unaffected by the blasts and turned on them, moving with surprising speed toward its attackers. "Whoa! That is _wicked_!" Karai remarked as they watched it. "How the heck am I gonna name _THIS_?!" Mikey asked helplessly. That monstrosity would be a challenge to name, even for a "pro at namin' stuff" like Mikey.

"Good question," Karai replied as she picked up the Krang-less upper half of a droid that was lying on the floor near her feet and slung it over her shoulder. "Well, see ya." She leaped up onto the vat, then through the air across to the upper walkway that went around the room and led to the elevators and stairs. She pushed a button on a panel near the double doors to open them.

"You're not gonna help us beat this thing?!" Leo yelled up to her. "It's _your_ fault!"

"I'll let the _heroes_ handle it!" she called, hoisting the droid half against her back.

"I...I _trusted_ you!"

"I know! That's messed up, right?" she acknowledged, and darted from the room.

Leo stood in shock. _I can't believe she just DID that!_ He blinked, and his vision was filled with the mutant monster's eyes, which were, unexpectedly, crackling with electricity. Krang-bots appeared on Leo's right and left, shooting at the creature to no avail. Its tentacles smashed them easily before coming after Leo. He sprinted around the room, avoiding the bolts of hot pink electricity now shooting from the monster's eyes.

As the other turtles watched their leader being chased around the lab for a few moments, Raph asked Mike and Donnie, "So, guys, we all fans of Karai yet?" Donnie could answer that easily: "I don't know who she is, but I know _I hate her_!" They all dodged the pink bolts now coming their way.

The Krang's laser blasts were all directed at the ferocious mutant; fighting the turtles could wait. Raph caught up to Leo and grinned sarcastically at him as they ran. "Hey look, Leo! The _Krang_ are on our side now!" Leo glared at him. " _Save_ it!"

They could only avoid the creature for so long. A long tentacle caught Raph by the foot and wrapped around his body, lifting him into the air and constricting him. Raph managed to break himself free with his sai and strength, and landed unhurt on the floor. "Nice try, octo-punk!" Raph yelled. It smacked him sideways into the wall.

That gave Mikey an idea. "No, No!" he exclaimed excitedly. "Call him...Octo-Eyeball-JELLY-Bug!" He blinked, and his enthusiasm deflated. "Ehhh...let's just call him Justin." A tentacle threw him aside. Donnie shrieked; one of "Justin's" pink lightening bolts had hit its mark and electrocuted him for several seconds. When the contact was broken, Donnie dropped to the floor with his eyes closed and tongue hanging out.

Leo looked at his brothers: Donnie lay unconscious; Raph and Mikey were groaning on the floor, still too stunned from being thrown into the wall to get up. Leo looked away and frowned. "Raph's right. It _is_ my fault."

Justin roared at Leo. Leo roared back, his eyes burning with rage. Justin looked startled.

Leo began running as the pink lightening, now anticipated, resumed shooting from Justin's eyes at him. Leo was too quick. He closed the gap between them and began striking the creature as hard and fast as he could, leaping back and forth to avoid the tentacles, and landing a hit or kick to its body with each pass.

A tentacle darted beneath Leo's feet and threw him high into the air of the cavernous room. On the way down, he crossed his swords over the top of the appendage and rode it like a zip-line all the way down to Justin's face (if it could be called a face). He landed on what he supposed was the top of its head and knocked it sideways so it hit the floor. The mutant was only stunned for a moment, but it gave Leo the opening he needed. By the time it righted itself he was in position.

"Hey, Justin!" He pointed a katana at it's head. "This ends now!"

As Leo expected, the monstrosity aimed its pink electro-ray at him. Leo caught the blast with his katana, his hand protected by the wood and leather of the hilt, and brought the hilt of his second katana to butt up against the first. Electricity surged through them both. Leo yelled with exertion as he stabbed the blade of the second sword into the console behind him, keeping both weapons perfectly aligned. The circuit closed, the electricity began surging through the console, the swords, and Justin's body into the floor.

Leonardo was thrown back as part of Justin's body exploded, but managed to land on his feet. What was left of the mutation was covered in green fire. It shrieked, ran into the wall, and disintegrated in a burst of smoke and flame.

Leo's mostly recovered brothers had gathered at his back. "HAH!" Mikey yelled and pointed at what was left of the monster. "Take THAT, Justin!"

The entire building shook; chunks of wall and ceiling began falling around them. The explosion was causing fires to break out and spread throughout the edifice. "C'mon, let's get out of here!" Leo called to his brothers, and led the way out of the burning structure.

The ninja made it to the fire escape of a building a safe distance from the flaming Worldwide Genome Project building. They watched as the fire burned through the roof and smoke poured into the night air. Sirens sounded in the distance. For a while, none of them said anything, but finally, Michelangelo, then Donatello, spoke up.

"Sooo..."

"We're thinking _somebody_ should start talking."

Leo closed his eyes and sighed. This was _not_ going to be fun.

…

 _I'm SURE they can handle that...thing._

Karai ran through the halls to the roof of the building, where she could escape unseen and get the Krang-bot she'd scavenged back to Foot headquarters.

 _I've seen them fight – I know they're good. They should be able to destroy it, easily_. At least, she hoped. But she certainly wouldn't have left Leonardo in a situation she thought he couldn't survive. _I have too much respect for him to do that_.

It wasn't the easiest thing, keeping out of sight and running silently with about sixty pounds of metal on her back, but she managed. _I have to get this to Baxter Stockman and Xever – TONIGHT. My father's already in a foul mood, and will be until Splinter – and the turtles – are dead. Who knows how many corpses he'll leave in his wake when he's like this? He raised me to fight – and kill – without mercy...but I can see no justification in such needless deaths, simply because he is impatient to get to Splinter._

Karai felt a twinge of regret creep into her thoughts. _Leo defended me...told his brother I was NOT bad news._ She sighed. _I guess he'll never see me that way again._

Her resolve grew stronger as she neared HQ. _Tonight wasn't about me. It was about saving two lives from wasteful_ deaths. She frowned. _I have no good name to uphold, anyway._

Karai bit her lip.

 _No matter what Leo thinks – or, thought - of me._

 _..._

 _..._

 _..._

 _..._

(Thanks for reading! Helpful feedback/advice welcomed and appreciated! The next chapter will conclude "The Alien Agenda." I hope you'll like it! Also, the first episode Karai was in, "New Girl in Town," is the first fanfic I wrote, and comes before this one. If you haven't read it yet, doing so might help "The Alien Agenda" make a little more sense, since I do occasionally reference Leo and Karai's first meetings. It's really optional, though, not necessary to understand this one (I hope). Thanks again for reading!)


	5. Mission Accomplished

**...**

 **TMNT – The Alien Agenda – Chapter 5 – Mission Accomplished**

…

(I hope you enjoy; feedback appreciated!)

...

Back at the lair, Leo hung his head in shame.

"...I should have told you about Karai sooner. But" - he couldn't help but smile hopefully - "I-I really thought there was a chance she would be good!" His smile faded, and he looked away from his family, dreading the last confession he was about to make. "And, I guess I...sort of...liked her."

Everyone watched him in silence.

"Go ahead...laugh."

"Dude, I can't believe you trusted her." Leo winced. Mikey always knew just what to say to make him feel better.

"I can't believe you didn't trust _us_ enough to tell us!" This rebuke from Donnie did seem well earned. After all, if there was one of his brothers Leo could trust to understand what it was like to be captivated by a young woman, it was Donatello.

"I was wrong. I'm _really_ sorry." _Sometimes the hardest part of being a leader is having to eat a big slice of humble pie – publically_.

"I tried to warn him," April shrugged. "You too, huh?" Raph replied with some satisfaction.

Splinter calmly stepped past April, Raph, Donnie, and Mikey, and stood before his eldest with his hands folded behind his back. "Leonardo: you are not the first young man, or turtle, to make a fool of yourself over a girl."

"What about Donnie?" Mikey interrupted. Donnie smacked him on the arm and glowered at him.

"However," Splinter said firmly, getting back to the subject at hand, "When that girl is a kunoichi in the employ of your enemy, that is an error you cannot afford." Leo hung his head and winced. It hurt to hear Splinter reprimand him, even – and especially – when it was deserved. _I hate disappointing him_. "Hai, Sensei."

"Deception is the ninja's most powerful weapon," Splinter continued, "and it seems Karai is a master."

"I know. We can't trust her; I see that now."

Splinter placed a fatherly hand on Leo's shoulder. "Good! You must learn from your mistake."

"Thank-you for understanding." Leo smiled as Splinter turned and slowly began to walk away. _This is actually going better than I thought_. "I'm glad you're not mad."

Splinter stopped in his tracks and looked over his shoulder sharply. His eyes narrowed. "Who says I'm not mad?!" He thumped the top of Leo's right foot with the base of his jade staff, then walked away.

" _YEOW!"_ Leo grabbed his throbbing foot and hopped in place for a moment before falling over onto the rug, yelping in pain. _Still...I probably am getting off pretty easy_ , he thought as he rubbed the blossoming bruise.

Later, as Leo was headed for bed, Raph caught up to him. "Hey, Bro..." Leo stopped and turned to face his brother. "I'm glad you came to your senses." Leo grinned and rubbed the back of his head sheepishly. "You were right. I don't know what I was thinking."

Raph grinned. "I can see how you think she's hot... In an...evil kind of a way..." he ceded.

Leo chuckled, then replied confidently, "Yeah. Well, don't worry. I am – _SO_ – over that."

Raph briefly gripped Leo's shoulder in understanding before walking to his own room, glad they were finally in agreement about Karai and could be cool again. He didn't see how after he turned away, Leo's face fell. For better or worse, Karai flooded his thoughts. It was involuntary. He _couldn't_ stop thinking about her.

Leo walked to his room, entered, and shut the door quietly behind him. Only one thing was on his mind. He went straight to his bed, lifted the mattress, and pulled out the tanto that lay hidden beneath it. The troubled ninja lowered the matress slowly, deep in thought, and sat on the edge of his bed, staring at the short sword in his hands. _But...she saved me_.

He closed his eyes, remembering that night. _So many times, she had me at her mercy;_ this _blade at my throat. And every time, she never harmed me and let me go. Not_ once _did she go in for the kill._ Opening his eyes, his strikingly blue irises focused on the crimson hilt, the dark metal blade. _She didn't have to save my life. But she did._ He shook his head confusedly. _How can someone who is SUPPOSED to be my enemy, yet defies her master's oath for vengeance over and over by letting me live, NOT be good?!_

The grip of one hand tightened on the hilt of her sword, the other grasping the blade until a thin red line appeared along his palm. _I_ can't _trust her, no matter how badly I want to. Even if there is some goodness in her, she's proven that she is loyal only to herself._

Leo reached over to his desk, grabbed a soft, dingy cloth he used for polishing his katana after sharpening them, and began to wipe the tanto clean of blood, dirt, fingerprints. He looked into the blackened surface and saw his reflection...until again, her face swam before his eyes. He blinked.

 _I may not be able to trust Karai._

 _But I refuse to hate her._

…

 _Here goes_.

Karai fixed her gaze straight ahead.

Her footfalls were so soft, no one in the throne room seemed to notice her approach, in spite of the slight metallic sound of the Krang-droid half slung across her back. Shredder watched, unamused, as Baxter Stockman struggled with the controles of Xever's robotic legs. Dogpound sat cross-legged on the floor, thumping his fist and laughing hysterically. "Oh-ho, this is too good! I could watch this forever!"

Xever's legs were walking, but facing backwards, smacking Xever's chin into the floor with every step. "Go...chase...AH!...a mailman!" Dopound howled with laughter. Baxter was beginning to panic. He fidgeted with the controls of the bulky remote console slung around his neck; when that didn't work, he shook it; hit it. He was running out of ideas, and Shredder wasn't going to put up with him for much longer.

Baxter nearly jumped out of his skin when Karai threw the Krang droid onto the large tool chest beside him. Everyone became quiet and looked at it, then her.

"The robots. I've seen them up close." Baxter immediately began inspecting the bot with great interest. "They call themselves the Krang."

"I told you, I am not interested in this robot-fiction!" Karai and Baxter looked up at the irate Shredder now stomping toward them. Baxter looked scared; Karai rolled her eyes. "I will hear _NO MORE_ of this!"

Karai smirked with one hand on her hip. In the other hand she held a thin, flat metal panel from the droid. "I think _this_ is how they control their robot bodies." She shrugged. "I don't know..." Her eyes cut over to Baxter. "...Maybe _you_ can use it?" _You'd better be able to, or I just wasted this night...and a possible friendship_. She tossed it over to the brainiac.

Baxter frowned at it with curiosity. Turning back to the bot, he pushed a button on the panel. The droid's head looked up with eyes and mouth illuminated. Baxter jumped back nervously. The push of another button caused the head to drop with a _bang_. He tried a different button; this time, an arm raised itself into the air at a twisted angle, then dropped. He looked down at the panel excitedly. "This is _exactly_ the sort of neural transmission interface I've been trying to develop!"

"Hmmm." Shredder's eyes narrowed as he considered the many possible uses of such advanced technology - both strategic, and lucrative. "Very well..." He walked behind Karai and placed his hands on her narrow shoulders while Baxter continued to play with the control panel, making the bot's limbs rise and fall. "I want you to find out all you can about this...Krang. Their technology may prove useful in our war against the turtles." His voice was low, gruff, and his tone grave, but it was the words he spoke next that she most wanted to hear. "...Well done, Karai."

Karai smiled darkly.

 _Mission accomplished._

…

Karai swung her feet absentmindedly over the edge of the Foot Clan HQ roof. The wind up there was stronger than on the streets below, and the air was fresher. She breathed deeply as her black sidelocks whipped her cheeks and jaw. The sun was just starting to rise, and the city was already seething with activity.

Her eyes stared into the ever-brightening sky, but she wasn't seeing it. Noise drifted up from the streets, now busy with pedestrians, taxis, delivery trucks, and pigeons, but she didn't hear it. An entirely different soundtrack was playing in her mind.

" _Nice going, Leo! You're protecting her? What is_ wrong _with you?! She is bad news!"_

" _No, she's not!"_

" _Yeah, I am."_

She sighed. _He must hate me now, after I left him in the middle of that fight._

" _Well, see ya."_

" _You're not gonna help us beat this thing? It's_ your _fault!"_

" _I'll let the_ heroes _handle it!"_

" _I...I_ trusted _you!"_

" _I know! That's messed up, right?"_

Karai closed her eyes and leaned back on her elbows, tilting her face to the sun to let the first, warm rays of the day wash over her features.

 _That is messed up. ...But, what choice did I have? Let a couple of my father's stupid henchmen die for no good reason? Sit back and watch as he continues to ignore the Krang, a threat to our entire species?_

She lay back on the roof like a black cat sunbathing, her arms resting at her sides. Her expression was peaceful, but her mind was racing.

 _Besides...I may have bought Leo some time. Now I have a new mission: learn everything I can about the Krang. Father wants their technology to help him defeat Splinter and the turtles, but at least in the meantime, hunting them down is no longer my sole purpose. And, if I'm being really honest with myself...I don't want to kill_ him _. Not Leo._

She remembered the look of joy on his face when she fought the Krang alongside him, and the pained disbelief in his eyes when she left him. She knew then how much he had wanted to believe in her. _I may hate his sensei, but I don't hate him._

 _...I'm not sure I ever can._

 _..._

 _..._

 _..._

 _..._

(Note from Author: Thank-you sooo much for reading! This concludes "The Alien Agenda." I hope you liked it! I try hard to make sure the parts I add to the story are very believable. I'm interested in knowing if you think so too, or if you think I'm way off the mark. My goal is not to change the original story line, but rather to make it fuller, deeper, and more well-rounded with insight. If you liked this, you might enjoy "New Girl in Town" as well. Keep an eye out for the next episode: "Enemy of My Enemy" (yes, Madelyn, I intend to write it; thanks for your support!). That one is going to be goooood (I hope); if you know the episode, you know there's ALL KINDS of things going on between Leo and Karai in it. It's begging to be written! Anyway, I've prattled long enough. Thanks again for reading!)


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